My Research Highlights

I recently study knowledge + LLM for scientific NLP.
In earlier years, I also studied multiple Machine Learning & AI for Science challenges.

PriORE: Open relation extraction with a priori relation generation

Organizing internal knowledge of LLMs into a structure to assist open RE.

EMNLP 2024

ORAG: Ontology-guided retrieval-augmented generation

Utilizing external knowledge to improves LLMs on focused topics.

COLM 2024

FGExpan: Taxonomy-guided fine-grained entity set expansion

Discovering entities from corpora with certain fine-grained types.

SDM 2023

Reader-retriever: Question answering through question space generation

Preparing for what may be asked before exams, or before performing QA.

NAACL SRW 2021

SetSearch: Intelligent biomedical literature search for entity set queries

Ranking research papers for complex queries without requiring labels.

SIGIR & KDD 2018

SigMat: Transfer learning for gene signature matching in less studied cell lines

Pre-training & fine-tuning, with linear models, before BERT made a hit.

ISMB & Bioinformatics 2018

Prostate cancer survival prediction project brief illustration

DWCox: Density-weighted Cox model for outlier-robust survival prognosis

Automatic weighting won a challenge where some teams did it manually.

F1000 Research 2016

Publications

* Equal contribution

Topic-Oriented Open Relation Extraction with A Priori Seed Generation

Linyi Ding*, Jinfeng Xiao*, Sizhe Zhou, Chaoqi Yang, Jiawei Han
EMNLP 2024

ORAG: Ontology-Guided Retrieval-Augmented Generation for Theme-Specific Entity Typing

Jinfeng Xiao*, Linyi Ding*, James Barry, Mohab Elkaref, Geeth De Mel, Jiawei Han
COLM 2024 [Paper]

Taxonomy-Guided Fine-Grained Entity Set Expansion

Jinfeng Xiao, Mohab Elkaref, Nathan Herr, Geeth De Mel, Jiawei Han
SDM 2023 [Paper]

Reader-Retriever Approach for Question Answering

Jinfeng Xiao, Lidan Wang, Franck Dernoncourt, Trung Bui, Tong Sun
U.S. Patent 2023 [Paper]

Open-Domain Question Answering with Pre-Constructed Question Spaces

Jinfeng Xiao, Lidan Wang, Franck Dernoncourt, Trung Bui, Tong Sun, Jiawei Han
NAACL SRW 2021 [Paper]

SigMat: A Classification Scheme for Gene Signature Matching

Jinfeng Xiao, Charles Blatti, Saurabh Sinha
ISMB & Bioinformatics 2018 [Paper] [Code]

SetSearch+: Entity-Set-Aware Search and Mining for Scientific Literature

Jiaming Shen*, Jinfeng Xiao*, Yu Zhang, Carl Yang, Jingbo Shang, Jinda Han, Saurabh Sinha, Peipei Ping, Richard Weinshilboum, Zhiyong Lu and Jiawei Han
KDD 2018 [Preprint] [System]

DWCox: A Density-Weighted Cox Model for Robust Prediction of Prostate Cancer Survival

Jinfeng Xiao, Sheng Wang, Jingbo Shang, Henry Lin, Doris Xin, Xiang Ren, Jiawei Han, Jian Peng
F1000Research 2016 [Paper] [Code]

Automated Construction of Theme-specific Knowledge Graphs

Linyi Ding, Sizhe Zhou, Jinfeng Xiao, Jiawei Han
arXiv 2024 [Code]

Reaction Miner: An Integrated System for Chemical Reaction Extraction from Textual Data

Ming Zhong et al.
EMNLP 2023 Demo [Paper] [Code]

Knowledge-Rich Self-Supervision for Biomedical Entity Linking

Sheng Zhang, Hao Cheng, Shikhar Vashishth, Cliff Wong, Jinfeng Xiao, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
EMNLP 2022 Findings [Paper]

ReactClass: Cross-Modal Supervision for Subword-Guided Reactant Entity Classification

Xuan Wang, Vivian Hu, Minhao Jiang, Yu Zhang, Jinfeng Xiao, Danielle Loving, Heng Ji, Martin Burke, Jiawei Han
BIBM 2022 [Paper]

ChemNER: Fine-Grained Chemistry Named Entity Recognition with Ontology-Guided Distant Supervision

Xuan Wang, Vivian Hu, Xiangchen Song, Shweta Garg, Jinfeng Xiao, Jiawei Han
EMNLP 2021 [Paper]

Fine-Grained Chemical Entity Typing with Multimodal Knowledge Representation

Chenkai Sun, Weijiang Li, Jinfeng Xiao, Nikolaus Parulian, Chengxiang Zhai, and Heng Ji
BIBM HiBB 2021 [Paper]

Scaling Up Data Science Course Projects: A Case Study

Bhavya Bhavya, Jinfeng Xiao and Chengxiang Zhai
L@S WiP 2021 [Paper]

Leveraging Personalized Sentiment Lexicons for Sentiment Analysis

Dominic Seyler, Jiaming Shen, Jinfeng Xiao, Yiren Wang, and ChengXiang Zhai
ICTIR 2020 [Paper]

Knowledge-Guided Analysis of "Omics" Data Using the KnowEnG Cloud Platform

Charles Blatti III et al.
PLoS Biology 2020 [Paper]

Query-Specific Knowledge Summarization with Entity Evolutionary Networks

Carl Yang, Lingrui Gan, Zongyi Wang, Jiaming Shen, Jinfeng Xiao and Jiawei Han
CIKM 2019 [Paper]

Stratification of Amyotrophic Lateral Sclerosis Patients: A Crowdsourcing Approach

Robert Kueffner et al.
Scientific Reports 2019 [Paper]

Entity Set Search of Scientific Literature: An Unsupervised Ranking Approach

Jiaming Shen, Jinfeng Xiao, Xinwei He, Jingbo Shang, Saurabh Sinha, Jiawei Han
SIGIR 2018 [Paper]

Large-Scale Integration of Heterogeneous Pharmacogenomic Data for Identifying Drug Mechanism of Action

Yunan Luo, Sheng Wang, Jinfeng Xiao, Jian Peng
PSB 2018 [Paper]

DPPred: An Effective Prediction Framework with Concise Discriminative Patterns

Jingbo Shang, Meng Jiang, Wenzhu Tong, Jinfeng Xiao, Jian Peng, Jiawei Han
IEEE TKDE 2018 [Paper]

A DREAM challenge to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer patients

Fatemeh Seyednasrollah et al.
JCO Clinical Cancer Informatics 2017 [Paper]

Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data

Justin Guinney et al.
Lancet Oncology 2017 [Paper]

Conference Presentations

Presentations on published papers are omitted.

Network-Guided Characterization of Drug-Specific Transcriptional Response in Cancer

Jinfeng Xiao, Charles Blatti, Saurabh Sinha
BD2K-LINCS Data Science Symposium 2017

Using Aggregated Weights Along Paths Across Random Forest to Select Important Features and Predict ALS Progression

Jinfeng Xiao, Jian Peng
RECOMB/ISCB RSG with DREAM 2015

Application of the Transition Probability Matrix to Colloidal Diffusion in a Periodic Energy Landscape

Jinfeng Xiao, Xiaoguang Ma, Penger Tong
Frontiers of Soft Matter Physics 2014

Gallery

Bring more fascination to the world around us.

We've covered everything about my work. Now, let’s switch gears and have some fun.

Want some music? How about I sing JJ Lin's Mermaid for you?

Embrace the world

I'm a global citizen. With over a decade of life beyond my beloved homeland, I have been leaving footprints across three continents. Shaped by both Eastern and Western cultures, I honor traditions, celebrate diversity, and find joy in life's vibrant tapestry.

Let imagination fly

I'm a coser. I love the thrill of immersing myself in a world of limitless imagination. I can do it all — sewing, makeup, hair styling, photography, and more. But the best part? I’m lucky to have amazing friends who embrace the same craziness with me.

Chase marvels

I'm a natural wonders enthusiast. 2024 gifted me with the rare opportunity to witness two aurora outbreaks and a total solar eclipse, all just a few hours' drive from my home in Illinois. These experiences were some of the moments when I felt truly fortunate.

Be my own chef

I'm a home cook. If you thought the sushi was from a fancy restaurant, think again — it's homemade! I make a wide range of authentic and inventive Chinese, Japanese, and American dishes. They’re tastier than what you'd find in most $-$$ restaurants!

Make cool videos

I am a multimedia editor. I turn photos and video clips into engaging short films. I’ve created videos for research groups and student organizations, and I’m active on video platforms. My content on Bilibili.com has garnered tens of thousands of views.

Reach hearts with words

I am a writer. My journey began at age 10 when I landed my first paid job as a magazine editor. The snapshot above is from my interview article (in Chinese) featuring UIUC alumnus Xiaohuang Huang, now CEO of Exacloud.